1 |
/* |
2 |
* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
3 |
* |
4 |
* The University of Notre Dame grants you ("Licensee") a |
5 |
* non-exclusive, royalty free, license to use, modify and |
6 |
* redistribute this software in source and binary code form, provided |
7 |
* that the following conditions are met: |
8 |
* |
9 |
* 1. Acknowledgement of the program authors must be made in any |
10 |
* publication of scientific results based in part on use of the |
11 |
* program. An acceptable form of acknowledgement is citation of |
12 |
* the article in which the program was described (Matthew |
13 |
* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
14 |
* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
15 |
* Parallel Simulation Engine for Molecular Dynamics," |
16 |
* J. Comput. Chem. 26, pp. 252-271 (2005)) |
17 |
* |
18 |
* 2. Redistributions of source code must retain the above copyright |
19 |
* notice, this list of conditions and the following disclaimer. |
20 |
* |
21 |
* 3. Redistributions in binary form must reproduce the above copyright |
22 |
* notice, this list of conditions and the following disclaimer in the |
23 |
* documentation and/or other materials provided with the |
24 |
* distribution. |
25 |
* |
26 |
* This software is provided "AS IS," without a warranty of any |
27 |
* kind. All express or implied conditions, representations and |
28 |
* warranties, including any implied warranty of merchantability, |
29 |
* fitness for a particular purpose or non-infringement, are hereby |
30 |
* excluded. The University of Notre Dame and its licensors shall not |
31 |
* be liable for any damages suffered by licensee as a result of |
32 |
* using, modifying or distributing the software or its |
33 |
* derivatives. In no event will the University of Notre Dame or its |
34 |
* licensors be liable for any lost revenue, profit or data, or for |
35 |
* direct, indirect, special, consequential, incidental or punitive |
36 |
* damages, however caused and regardless of the theory of liability, |
37 |
* arising out of the use of or inability to use software, even if the |
38 |
* University of Notre Dame has been advised of the possibility of |
39 |
* such damages. |
40 |
*/ |
41 |
|
42 |
#include "applications/dynamicProps/RadialRCorrFunc.hpp" |
43 |
|
44 |
|
45 |
namespace oopse { |
46 |
RadialRCorrFunc::RadialRCorrFunc(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2) |
47 |
: ParticleTimeCorrFunc(info, filename, sele1, sele2, DataStorage::dslPosition){ |
48 |
|
49 |
setCorrFuncType("RadialRCorrFunc"); |
50 |
setOutputName(getPrefix(dumpFilename_) + ".r_rcorr"); |
51 |
|
52 |
frameCentroid_ = new SnapshotCentroid(info,filename); |
53 |
|
54 |
} |
55 |
|
56 |
RealType RadialRCorrFunc::calcCorrVal(int frame1, int frame2, StuntDouble* sd1, StuntDouble* sd2) { |
57 |
RealType r0; |
58 |
RealType rt; |
59 |
Vector3d coord_t0; |
60 |
Vector3d coord_t; |
61 |
|
62 |
Vector3d r1 = sd1->getPos(frame1); |
63 |
Vector3d r2 = sd2->getPos(frame2); |
64 |
Vector3d com1 = frameCentroid_->getFrameCOM(frame1); |
65 |
Vector3d com2 = frameCentroid_->getFrameCOM(frame2); |
66 |
|
67 |
coord_t0 = r1 - com1; |
68 |
coord_t = r2 - com2; |
69 |
|
70 |
return (coord_t - coord_t0).lengthSquare(); |
71 |
} |
72 |
|
73 |
} |